Michel,
If you change the .bui file directly by text editor (or GenOpt), will Type 56 realize that the .trn file containing the transfer functions of the walls is not up to date anymore and recalculate them? If it doesn't you might have a problem with this approach.
Yes. In TRNSYS 16, TRNBuild is always launched at the beginning of a simulation that includes Type 56. It opens the BUI file and regenerates the TRN, BLD and INF files. So any change in the BUI (by GenOpt or any other means) will be reflected in the simulation. Another advantage of that (and the main reason for doing it I think) is that you don't have to include the TRN and BLD files if you want to share your project and you don't have to worry about mismatches between TRNBuild and Type56 versions. Data from the window library (the (in)famous w4-lib.dat) is also included in the BUI file itself so you don't need to worry about another user having different libraries either.
Michaël Kummert University of Strathclyde Dept. of Mechanical Engineering Energy Systems Research Unit